BN1975 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 8.9215e-07 3.6575e-05
Layer 3 2.2129e-06 1.2020e-03
Layer 5 4.5709e-05 1.6403e-03
Layer 2 4.9517e-05 1.4927e-01
Layer 6 2.0796e-04 4.1022e-03
WM 2.5782e-01 3.3449e-01
Layer 1 7.7209e-01 6.5683e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.1318 0.7042
SYNGR1 Layer 4 2.3086 0.6493
APBA2 Layer 4 2.5176 0.6483
NUDT4 Layer 4 2.5000 0.6460
SH3GL2 Layer 4 2.2363 0.6447
CEND1 Layer 5 2.2363 0.6410
TUBA4A Layer 4 2.2617 0.6344
PFKP Layer 5 2.5000 0.6325
CPLX1 Layer 4 2.3555 0.6310
GOT1 Layer 4 2.3555 0.6274
STMN2 Layer 5 2.1621 0.6239
NUAK1 Layer 4 2.2324 0.6236
RAB3A Layer 4 2.1152 0.6228
PRKCZ Layer 5 2.1445 0.6197
KLHDC3 Layer 4 2.2969 0.6190
DNAJC6 Layer 4 2.3027 0.6153
CALY Layer 4 2.1680 0.6153
NAPEPLD Layer 4 2.5215 0.6135
NDRG4 Layer 4 2.1914 0.6106
TTC9B Layer 5 2.4863 0.6102
ATP6AP1 Layer 4 2.2773 0.6099
AP2S1 Layer 5 2.1289 0.6095
NAP1L5 Layer 4 2.3398 0.6093
PRDX2 Layer 4 2.1582 0.6086
YPEL5 Layer 4 2.4395 0.6080
UBE2N Layer 4 2.0781 0.6063
PGK1 Layer 4 2.2969 0.6056
CHGA Layer 4 2.5176 0.6031
SLC6A17 Layer 4 2.5449 0.6023
PITHD1 Layer 5 2.0625 0.6021
NEUROD2 Layer 3 2.0391 0.6020
TUBB2A Layer 5 2.0039 0.6018
COX5A Layer 4 2.2969 0.6015
PDXP Layer 4 2.1777 0.6000
ATP6V0B Layer 4 2.0684 0.5979
SELENOH Layer 4 2.3242 0.5973
VCP Layer 4 2.2520 0.5961
GNG3 Layer 5 2.1582 0.5957
SNAP91 Layer 4 2.2969 0.5955
RUSC1 Layer 4 2.2832 0.5949
MAP1A Layer 5 1.8887 0.5948
CAMK2G Layer 4 2.4180 0.5917
ELAVL4 Layer 5 2.1816 0.5913
SSBP3 Layer 4 2.3242 0.5911
ATP6V0A1 Layer 4 2.2324 0.5900
TUBB4B Layer 5 2.0215 0.5893
CDC37 Layer 4 2.5566 0.5889
ATP5MC3 Layer 4 2.1348 0.5884
NEDD8 Layer 6 1.9678 0.5883
NISCH Layer 4 2.1094 0.5874

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1975
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1975_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1975/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1975/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1975/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1975/report/PD/BN1975_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1975/report/PD/BN1975_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:34:01
  • Number of Processes: 10
  • Spending Time: 0h 3m